Evidence map›Paper›PMID 37790540›Full record

ArticlemedRxiv : the preprint server for health sciences2023

Smoking-informed methylation and expression QTLs in human brain and colocalization with smoking-associated genetic loci.

Megan Ulmer Carnes, Bryan C Quach, Linran Zhou, Shizhong Han, Ran Tao, Meisha Mandal, Amy Deep-Soboslay, Jesse A Marks, Grier P Page, Brion S Maher and 7 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 1 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors at 5 institutions in 1 country.

Megan Ulmer CarnesGenomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina.
Bryan C QuachGenomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina.
Linran ZhouGenomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina.
Shizhong HanLieber Institute for Brain Development (LIBD), Baltimore, Maryland.
Ran TaoLieber Institute for Brain Development (LIBD), Baltimore, Maryland.
Meisha MandalGenomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina.
Amy Deep-SoboslayLieber Institute for Brain Development (LIBD), Baltimore, Maryland.
Jesse A MarksGenomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina.
Grier P PageGenomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina.
Brion S MaherDepartment of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, Maryland.
Andrew E JaffeLieber Institute for Brain Development (LIBD), Baltimore, Maryland.
Hyejung WonDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
Laura J BierutDepartment of Psychiatry, Washington University in St. Louis, Missouri.
Thomas M HydeLieber Institute for Brain Development (LIBD), Baltimore, Maryland.
Joel E KleinmanLieber Institute for Brain Development (LIBD), Baltimore, Maryland.
Eric O JohnsonGenomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina.
Dana B HancockGenomics and Translational Research Center, RTI International, Research Triangle Park, North Carolina.
RTI International · USLieber Institute for Brain Development · USJohns Hopkins University · USUniversity of North Carolina at Chapel Hill · USWashington University in St. Louis · US

Funding

Integrating Epigenomics in Human Brain and Genomics of Nicotine DependenceR01DA042090 · NIDA · RESEARCH TRIANGLE INSTITUTE · PI HANCOCK, DANA B · 2016 to 2020
$3.5M
Integrating Multiple Omics to Illuminate Gene Networks Underlying Cigarette Smoking and Opioids.R01DA051913 · NIDA · RESEARCH TRIANGLE INSTITUTE · PI HANCOCK, DANA B, JACOBSON, DANIEL A · 2020 to 2024
$2.9M
Using H-MAGMA to decipher neurobiological bases of smoking and alcohol use traitsR21DA051921 · NIDA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI WON, HYEJUNG · 2020 to 2021
$453k
NIDA NIH HHS R01 DA042090NIDA NIH HHS R01 DA051913NIDA NIH HHS R21 DA051921
6 · The paper itself

Abstract

Smoking is a leading cause of preventable morbidity and mortality. Smoking is heritable, and genome-wide association studies (GWAS) of smoking behaviors have identified hundreds of significant loci. Most GWAS-identified variants are noncoding with unknown neurobiological effects. We used genome-wide genotype, DNA methylation, and RNA sequencing data in postmortem human nucleus accumbens (NAc) to identify cis-methylation/expression quantitative trait loci (meQTLs/eQTLs), investigate variant-by-cigarette smoking interactions across the genome, and overlay QTL evidence at smoking GWAS-identified loci to evaluate their regulatory potential. Active smokers (N=52) and nonsmokers (N=171) were defined based on cotinine biomarker levels and next-of-kin reporting. We simultaneously tested variant and variant-by-smoking interaction effects on methylation and expression, separately, adjusting for biological and technical covariates and using a two-stage multiple testing approach with eigenMT and Bonferroni corrections. We found >2 million significant meQTL variants (p

Identifiers

PMID37790540
PMCPMC10543041
OpenAlexW4386935642

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.